MBMB 451A Section One - Fall 2007

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Supercoiling of DNA

1.  Topology figure 29-17
	A.  Right handed supercoiling = negative supercoiling (underwinding)
	B.  Left handed supercoiling = positive supercoiling
	C.  Relaxed state is with no bends figure 29-18
	D.  DNA must be constrained: plasmid DNA or by proteins
	E.  Unraveling the DNA at one position changes the superhelicity -
	F.  Topology only defined for continuous deformation - no strand breakage
	

2.  Numerical expression for degree of supercoiling
	A.  Equation 	Lk=Tw+Wr
	B.  L:linking number, # of times that one DNA strand winds about the others strands, is always an integer
	 	figure 29-18 and 29-19 
	C.  T: twist,# of revolutions about the duplex helix  figure 29-19 
	D.  W: writhe, # of turns of the duplex axis about the superhelical axis
	      is by definition the measure of the degree of supercoiling
	E.  specific linking difference or superhelical density=DLk/Lk0 				
	

3.  Methods for measuring supercoiling - based on how compact the DNA is
	A.  Gel electrophoresis
		i.   1 dimensional figure 29-24
		ii.  2 dimensional 
	B.  Density sedimentation figure 29-22

4.  Topoisomerases are required to relieve torsional strain
	A.  Topoisomerases I - breaks only one strand figure 29-25a and b
		i.  monomeric protein
		ii. after nicking DNA the 5'-PO4 is covalently linked to enzyme (prokaryotes)
  		    or the 3' end is linked to the enzyme (eukaryotes)
		iii.  evidence is the formation of catenates
		iv.  E. coli Topo I relaxes negatively supercoiled DNA
		v.  introduces a change of increments of 1 in writhe
	B.  Topoisomerase II figure 29-30
		i.  supercoils DNA at the expense of ATP hydrolysis
		ii.  two subunits: (alpha)2 and (beta)2
		iii.  becomes covalently linked to the alpha subunit
		iv.  relaxes both negative and positively supercoiled DNA
		v.  introduces a change in increments of 2 in writhe.
	

5.  DNA compaction require special form of supercoiling
	A.  Interwound - supercoiling of DNA in solution
	B.  Toroidal- tight left handed turns, packing of DNA
	     both forms are interconvertible  figure 29-21

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Nucleic Acids  |  Methods-Nucleic Acids: Part A and Part B  |  Protein Methods  |  Nucleosome  | Transcription: Part A and Part B  | 
Higher Ordered Structure  |  Chromatin Transcription  |  Regulation of Transcription  |  Course Material

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Last updated on August 30, 2007.